No issues doing it next Spring. We would wait.

It is either mildew to rust. Either way you would need to strip and start over to fix.

We would need pictures. Also, you should have treated this as new wood and you over sanded too smooth:

We have no idea how flammable wood is and why would it matter? The deck is already there. The stain does not increase the flammability once dried.

Go ahead and stain. No need to redo the prep.

Once the stain has cured, not any different than if unstained.

AC I believe does not contain a fire retardant anymore and we have no experience with using them.

No, not related in any way. TWP is made by Gemini Coatings in Oklahoma and AC is made by Armstong Clark in California. The sites you are referring ...

Damp or dry is fine.

Damp or dry is fine.

Clear has no UV protection from graying. Must be tinted. See here about new wood tips:

You cannot strip this off. As we mentioned earlier, the only way to fix this is to 100% sand it off. Sounds like he did not do this and made it worse ...

You need to use the Gemini Restore A Deck Kits while pressure washing for prep: Pressure washing alone is not proper prep.

The wood was probably wet internally and then stain could not soak in. You will need to remove all 100% to fix and start over.

Wait for 48 hours after rain to stain the deck.